I have been cleaning up all my indexes so that when I search for a tune, and click it, it goes to the correct page. I have set all my off-sets so that the first tune of each book is correct. Problem is several of my pdf books have pages missing throughout (usually because the pictures were skipped when scanning). I was able to fix this problem with several of my books by using Adobe Acrobat Pro to simply add a blank page where needed. Now I realize that some of my pdf book collection is "Secure", whoever created it put password security on the document, so I am unable to add a blank page.

Is there a way I can adjust the index so it matches my pdf, or any other suggestion to fix this problem?

You can't alter indexes we provide and we don't provide index data for you to manipulate. If the PDF allows printing, you can always print it to a PDF and add or rearrange the pages that you need. You could also use the Set List Sharing feature to generate a PDF of the "Secured PDF" and make changes to that, if it in face will print.